Computer programs for visualizations using image data and predefined data of surgical tools

ABSTRACT

Circuits and computer program products onboard and/or adapted to communicate with an scanner that electronically recognize predefined physical characteristics of the at least one tool to automatically segment image data provided by the scanner whereby the at least one tool constitutes a point of interface with the system. The circuits and computer program products are configured to provide a User Interface that defines workflow progression for an image guided surgical procedure and allows a user to select steps in the workflow, and generate multi-dimensional visualizations using the predefined data of the at least one tool and data from images of the patient in substantially real time during the surgical procedure.

RELATED APPLICATIONS

This application is a continuation application (an indirect divisionalapplication) of U.S. patent application Ser. No. 13/610,338, filed Sep.11, 2012, which is a first divisional application of U.S. patentapplication Ser. No. 12/236,854, filed Sep. 24, 2008, which is acontinuation-in-part of U.S. application Ser. No. 12/134,412, filed Jun.6, 2008, which issued on May 8, 2012 as U.S. Pat. No. 8,175,677, andwhich also claims priority to U.S. Provisional Application Ser. No.60/974,821, filed Sep. 24, 2007, the contents of which are herebyincorporated by reference as if recited in full herein.

FIELD OF THE INVENTION

The present invention relates to MRI-guided diagnostic or interventionalsystems that may be particularly suitable for placement/localization ofinterventional medical devices and/or therapies in the body. Embodimentsof the present invention may be particularly suitable for placingneuromodulation leads, such as Deep Brain Stimulation (“DBS”) leads,placing implantable parasympathetic or sympathetic nerve chain leadsand/or CNS stimulation leads and/or for delivering therapies to targetinternal locations in the body including atrial fibrillation (AFIB)therapies.

BACKGROUND OF THE INVENTION

Deep Brain Stimulation (DBS) is becoming an acceptable therapeuticmodality in neurosurgical treatment of patients suffering from chronicpain, Parkinson's disease or seizure, and other medical conditions.Other electro-stimulation therapies have also been carried out orproposed using internal stimulation of the sympathetic nerve chainand/or spinal cord, etc.

One example of a prior art DBS system is the Activa® system fromMedtronic, Inc. The Activa® system includes an implantable pulsegenerator stimulator that is positioned in the chest cavity of thepatient and a lead with axially spaced apart electrodes that isimplanted with the electrodes disposed in neural tissue. The lead istunneled subsurface from the brain to the chest cavity connecting theelectrodes with the pulse generator. These leads can have multipleexposed electrodes at the distal end that are connected to conductorswhich run along the length of the lead and connect to the pulsegenerator placed in the chest cavity.

It is believed that the clinical outcome of certain medical procedures,particularly those using DBS, may depend on the precise location of theelectrodes that are in contact with the tissue of interest. For example,to treat Parkinson's tremor, DBS stimulation leads are conventionallyimplanted during a stereotactic surgery, based on pre-operative MRI andCT images. These procedures can be long in duration and may have reducedefficacy as it has been reported that, in about 30% of the patientsimplanted with these devices, the clinical efficacy of thedevice/procedure is less than optimum.

SUMMARY OF EMBODIMENTS OF THE INVENTION

Some embodiments of the present invention are directed to MRI-guidedsystems that can generate substantially real time patient-specificvisualizations of the patient and one or more surgical tools in logicalspace and provide feedback to a clinician to improve the speed and/orreliability of an intrabody procedure.

The visualizations can be based (in-part) on predefined data of thetool(s) which define a point of interface for the system (e.g.,software) based on predefined characteristics of the tool(s), e.g.,dimensions, shape or configuration and/or known rotational,translational and/or other functional and/or dynamic behavior of one ormore surgical tools. The visualizations can include patient functiondata (e.g., fMRI data, electrical activity, active regions of a brainduring a defined stimulation, fiber tracks, and the like).

The system can be configured to interrogate and segment image data tolocate fiducial markers and generate successive visualizations of thepatient's anatomical structure and tool(s) using MRI image data and apriori data of the tool(s) to provide (substantially real-time)visualizations of the patient.

Some embodiments are directed to MRI-guided surgical systems. Thesystems include: (a) at least one MRI-compatible surgical tool; (b) acircuit adapted to communicate with an MRI scanner; and (c) at least onedisplay in communication with the circuit. The circuit electronicallyrecognizes predefined physical characteristics of the at least one toolto automatically segment MR image data provided by the MRI scannerwhereby the at least one tool constitutes a point of interface with thesystem. The circuit is configured to provide a User Interface thatdefines workflow progression for an MRI-guided surgical procedure andallows a user to select steps in the workflow, and wherein the circuitis configured to generate multi-dimensional visualizations using thepredefined data of the at least one tool and data from MRI images of thepatient in substantially real time during the surgical procedure.

Other embodiments are directed to methods for performing an MRI-guidedsurgical procedure. The methods include: (a) defining dimensional and/orfunctional data of at least one MRI compatible surgical tool; (b)obtaining MRI image data of the patient; (c) electronically segmentingthe MRI image data to identify known fiducial markers on the at leastone tool based on the defining step; (d) generating visualizations ofthe at least one tool registered to patient anatomical structure; (e)electronically generating directions on adjustments for a pitch, roll orX-Y actuator to adjust a trajectory of a trajectory guide; and (f)guiding the tool to a location in the patient using patient MRI imagedata, the directions for adjustment and the visualizations therebyfacilitating an MRI-guided surgical procedure.

Still other embodiments are directed to computer program products forfacilitating an MRI-guided surgical procedure. The computer programproduct includes a computer readable storage medium having computerreadable program code embodied in the medium. The computer-readableprogram code includes: (a) computer readable program code that comprisespredefined physical data of a plurality of different surgical tools; (b)computer readable program code that communicates with an MRI scanner toobtain MRI image data of a patient; and (c) computer readable programcode that generates visualizations of the patient using data from thetools and the image data of the patient in substantially real-time.

Yet other embodiments are directed to MRI-guided interventional deepbrain systems. The systems include: (a) an MRI Scanner; (b) a clinicianworkstation with a circuit and a display, the workstation incommunication with the MRI Scanner; (c) at least one flexible patch witha grid thereon configured to releasably attach to a patient's skull; and(d) at least one trajectory guide attachable to a skull of a patient.The guide has a base with an aperture configured to reside over a burrhole formed in a patient's skull. The base aperture provides amechanical center of rotation for a pivot axis associated with thetrajectory guide, the base having a plurality of fiducial markers spacedapart about the base aperture. The circuit comprises physical dataregarding the patch and is configured to interrogate patient imagingdata provided by the MRI Scanner and segment the image data to define aburr hole location that intersects the patch with a desired intrabraintrajectory. The circuit comprises tool-specific data of the trajectoryguide and is configured to interrogate patient imaging data provided bythe MRI Scanner and interactively generate visualizations of thepatient's brain and the trajectory guide to the display.

In some embodiments, the circuit is configured to provide a defaulttrajectory for the trajectory guide on the display that extends througha center location of the grid patch.

Embodiments of the invention can provide output to a user such as one ormore of: (a) electronic generated warnings to alert an improper plannedtrajectory for a trajectory guide; (b) warnings regarding a physicalinterference with a planned projected trajectory associated with the MRIbore size and (isocenter) position (and optionally, patient head sizeand angle(s) or configuration of a surgical tool); (c) electronicinstructions on what grid entry location to use to obtain a desiredtrajectory or entry point into the patient brain; (d) calculate andprovide suggested physical adjustments to actuators to obtain a desiredtrajectory orientation and generate instructions on what adjustments tomake to X, Y, pitch and roll adjustment mechanisms (e.g., rotate Xbutton or dial left or right, potentially with a number of rotations orincrements and the like) associated with the trajectory guide to obtainthe desired trajectory; and (e) generate electronic data of electrodeoffset values for stimulation leads in the brain to define where theelectrodes are anatomically positioned whereby pulse generatorprogramming may be accelerated over conventional techniques.

Some embodiments of the present invention can provide visualizations toallow more precise control, delivery, and/or feedback of a therapy sothat the therapy or a tool associated therewith can be more preciselyplaced, delivered, confirmed and visualized.

These and other embodiments will be described further below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic illustration of a MRI-guided surgical systemaccording to some embodiments of the present invention.

FIG. 2 is a schematic illustration of an MRI-guided surgical system withMRI compatible cameras according to embodiments of the presentinvention.

FIG. 3 is a schematic illustration of an MRI-guided surgical systemaccording to some embodiments of the present invention.

FIG. 4 is a schematic illustration of an exemplary screen shot of a userinterface according to some embodiments of the present invention.

FIG. 5 is a schematic of exemplary disposable hardware that can be usedto carryout embodiments of the present invention.

FIG. 6A is a schematic of an exemplary trajectory guide in position on apatient according to some embodiments of the present invention.

FIG. 6B is a side view of a depth stop with a cooperating elongatemember according to some embodiments of the present invention.

FIG. 6C is a side view of a depth stop cooperating with an elongatemember and peel-away sheath according to some embodiments of the presentinvention.

FIG. 6D is a side perspective view of the depth stop and sheathcooperating with the trajectory guide according to some embodiments ofthe present invention.

FIG. 7 is a side perspective view of a trajectory guide and optionalcamera device according to some embodiments of the present invention.

FIG. 8 is a sectional view of the trajectory guide with a targetingcanula according to some embodiments of the present invention.

FIG. 9 is a top view of a base of a trajectory guide with fiducialsaccording to some embodiments of the present invention.

FIG. 10 is a side perspective view of the base shown in FIG. 9.

FIG. 11 is a schematic illustration of a marking grid patch andassociated screen display of coordinates of a surgical entry siteaccording to embodiments of the present invention.

FIGS. 12A-12E are schematic illustrations of grid segmentation and griddeformation that can be used to define an entry site location accordingto embodiments of the present invention.

FIGS. 13A-13C are schematic illustrations of a base or frame markersegmentation that can be used to define position and orientation of abase or frame of a trajectory guide according to embodiments of thepresent invention.

FIGS. 14A and 14B are illustrations of a User Interface (UI) tool barwith exemplary workflow groups according to embodiments of the presentinvention. FIG. 14B illustrates UI selectable steps for a selectedworkflow group according to some embodiments of the present invention.

FIG. 15 is a screen shot of an exemplary (e.g., DBS) workstation Startwindow for a workstation display according to embodiments of the presentinvention.

FIGS. 16-19 and 22-38 are screen shots of exemplary displays ofdifferent workflow groups and/or steps associated with a User Interfaceprovided to a user to facilitate an MRI-guided procedure.

FIGS. 20 and 21 are examples of operational warnings provided to aworkstation/display that can be automatically generated by the systemaccording to some embodiments of the present invention.

FIG. 39 is a data processing system according to some embodiments of thepresent invention.

DETAILED DESCRIPTION OF EMBODIMENTS OF THE INVENTION

The present invention will now be described more fully hereinafter withreference to the accompanying drawings, in which embodiments of theinvention are shown. This invention may, however, be embodied in manydifferent forms and should not be construed as limited to theembodiments set forth herein; rather, these embodiments are provided sothat this disclosure will be thorough and complete, and will fullyconvey the scope of the invention to those skilled in the art. Likenumbers refer to like elements throughout. It will be appreciated thatalthough discussed with respect to a certain embodiment, features oroperation of one embodiment can apply to others.

In the drawings, the thickness of lines, layers, features, componentsand/or regions may be exaggerated for clarity and broken lines (such asthose shown in circuit of flow diagrams) illustrate optional features oroperations, unless specified otherwise. In addition, the sequence ofoperations (or steps) is not limited to the order presented in theclaims unless specifically indicated otherwise.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. It will be further understood that the terms “comprises”and/or “comprising,” when used in this specification, specify thepresence of stated features, steps, operations, elements, and/orcomponents, but do not preclude the presence or addition of one or moreother features, steps, operations, elements, components, and/or groupsthereof. As used herein, the term “and/or” includes any and allcombinations of one or more of the associated listed items.

Unless otherwise defined, all terms (including technical and scientificterms) used herein have the same meaning as commonly understood by oneof ordinary skill in the art to which this invention belongs. It will befurther understood that terms, such as those defined in commonly useddictionaries, should be interpreted as having a meaning that isconsistent with their meaning in the context of the specification andrelevant art and should not be interpreted in an idealized or overlyformal sense unless expressly so defined herein. Well-known functions orconstructions may not be described in detail for brevity and/or clarity.

It will be understood that when a feature, such as a layer, region orsubstrate, is referred to as being “on” another feature or element, itcan be directly on the other element or intervening elements may also bepresent. In contrast, when an element is referred to as being “directlyon” another feature or element, there are no intervening elementspresent. It will also be understood that, when a feature or element isreferred to as being “connected” or “coupled” to another feature orelement, it can be directly connected to the other element orintervening elements may be present. In contrast, when a feature orelement is referred to as being “directly connected” or “directlycoupled” to another element, there are no intervening elements present.Although described or shown with respect to one embodiment, the featuresso described or shown can apply to other embodiments.

The term “electroanatomical visualization” or refers to a visualizationor map of the anatomical structure, e.g., brain or heart, typically avolumetric, 3-D map or 4-D map, that illustrates or shows electricalactivity of tissue correlated to anatomical and/or coordinate spatialposition. The visualization can be in color and color-coded to providean easy to understand map or image with different measures or gradientsof activity in different colors and/or intensities. The term“color-coded” means that certain features electrical activity or otheroutput are shown with defined colors of different color and/or intensityto visually accentuate different tissue, different and similarelectrical activity or potential in tissue and/or to show abnormalitiesor lesions in tissue versus normal or non-lesion tissue. In someembodiments, the systems can be configured to allow a clinician toincrease or decrease the intensity or change a color of certain tissuetypes or electrical outputs, e.g., in high-contrast color and/orintensity, darker opacity or the like.

The actual visualization can be shown on a screen or display so that themap and/or anatomical or tool structure is in a flat 2-D view and/or in2-D what appears to be 3-D volumetric images with data representingfeatures or electrical output with different visual characteristics suchas with differing intensity, opacity, color, texture and the like. A 4-Dmap illustrates time-dependent activity, such as electrical activity orblood flow movement.

The systems are configured to operate based on known physicalcharacteristics of one or more surgical tools such that the hardware isa point of interface for the circuit or software. The systems cancommunicate with databases that define dimensions, configurations orshapes and spacing of components on the tool(s). The defined physicaldata can be obtained from a CAD model of a tool. The physicalcharacteristics can include dimensions or other physical features orattributes and may also include relative changes in position of certaincomponents or features upon a change in position of a tool or portionthereof. The defined physical characteristics can be electronically(programmatically) accessible by the system or known a priori andelectronically stored locally or remotely and used to automaticallycalculate certain information and/or to segment image data. That is, thetool data from the model can be used to segment image data and/orcorrelate a position and orientation of a tool and/or provide trajectoryadjustment guidelines or error estimates, warnings of impropertrajectories and the like. For example, a grid for marking a burr holelocation and/or a trajectory guide that adjusts an intrabrain path forplacing a diagnostic or therapy device and such can be input,transposed, and/or overlayed in a visualization of the tool and patientstructure or otherwise used, such as, for example, to project theinformation onto a patient's anatomical structure or determine certainoperational parameters including which image volume to obtain highresolution MRI image data that include select portions of the targetingcanula. At least some of the resulting visualizations are not merely anMRI image of the patient during a procedure.

The visualizations are rendered visualizations that can combine multiplesources of data to provide visualizations of spatially encoded toolposition and orientation with anatomical structure and can be used toprovide position adjustment data output so that a clinician can move acontroller a certain amount to obtain a desired trajectory path, therebyproviding a smart-adjustment system without requiring undue “guess” workon what adjustments to make to obtain the desired trajectory.

The term “animation” refers to a sequence or series of images shown insuccession, typically in relatively quick succession, such as in about1-50 frames per second. The term “frame” refers to a singlevisualization or static image. The term “animation frame” refers to oneimage frame of the different images in the sequence of images. The term“ACPC coordinate space” refers to a right-handed coordinate systemdefined by anterior and posterior commissures (AC, PC) and Mid-Sagittalplane points, with positive directions corresponding to a patient'sanatomical Right, Anterior and Head directions with origin at themid-comissure point.

The term “grid” refers to a pattern of crossed lines or shapes used as areference for locating points or small spaces, e.g., a series of rowsand intersecting columns, such as horizontal rows and vertical columns(but orientations other than vertical and horizontal can also be used).The grid can include associated visual indicia such as alphabeticalmarkings (e.g., A-Z and the like) for rows and numbers for columns(e.g., 1-10) or the reverse. Other marking indicia may also be used. Thegrid can be provided as a flexible patch that can be releasably attachedto the skull of a patient. For additional description of suitable griddevices, see co-pending, co-assigned U.S. patent application Ser. No.12/236,621.

The term “fiducial marker” refers to a marker that can be electronicallyidentified using image recognition and/or electronic interrogation ofMRI image data. The fiducial marker can be provided in any suitablemanner, such as, but not limited to, a geometric shape of a portion ofthe tool, a component on or in the tool, a coating or fluid-filledcomponent or feature (or combinations of different types of fiducialmarkers) that makes the fiducial marker(s) MRI-visible with sufficientsignal intensity (brightness) for identifying location and/ororientation information for the tool and/or components thereof in space.

The term “RF safe” means that the lead or probe is configured to safelyoperate when exposed to RF signals, particularly RF signals associatedwith MRI systems, without inducing unplanned current that inadvertentlyunduly heats local tissue or interferes with the planned therapy. Theterm “MRI visible” means that the device is visible, directly orindirectly, in an MRI image. The visibility may be indicated by theincreased SNR of the MRI signal proximate the device.

The system can include an intrabody MRI receive imaging probe antenna tocollect signal from local tissue. The term “MRI compatible” means thatthe so-called component(s) is safe for use in an MRI environment and assuch is typically made of a non-ferromagnetic MRI compatible material(s)suitable to reside and/or operate in a high magnetic field environment.The term “high-magnetic field” refers to field strengths above about 0.5T, typically above 1.0 T, and more typically between about 1.5 T and 10T. MRI Scanners are well known and include high-field closed bore andopen bore systems.

Embodiments of the present invention can be configured to carry outdiagnostic and interventional procedures such as to guide and/or placeinterventional devices to any desired internal region of the body orobject, but may be particularly suitable for neurosurgeries. The objectcan be any object, and may be particularly suitable for animal and/orhuman subjects. Although primarily described with respect to placementof stimulation leads in the brain, the invention is not limited thereto.For example, the system can be used for gene and/or stem-cell basedtherapy delivery or other neural therapy delivery and allow user-definedcustom targets in the brain or to other locations. In addition,embodiments of the systems can be used to ablate tissue in the brain orother locations. In some embodiments, it is contemplated that thesystems can be configured to treat AFIB in cardiac tissue, and/or todeliver stem cells or other cardio-rebuilding cells or products intocardiac tissue, such as a heart wall, via a minimally invasive MRIguided procedure while the heart is beating (i.e., not requiring anon-beating heart with the patient on a heart-lung machine).

Examples of known treatments and/or target body regions are described inU.S. Pat. Nos. 6,708,064; 6,438,423; 6,356,786; 6,526,318; 6,405,079;6,167,311; 6,539,263; 6,609,030 and 6,050,992, the contents of which arehereby incorporated by reference as if recited in full herein.

Embodiments of the present invention may take the form of an entirelysoftware embodiment or an embodiment combining software and hardwareaspects, all generally referred to herein as a “circuit” or “module.” Insome embodiments, the circuits include both software and hardware andthe software is configured to work with specific hardware with knownphysical attributes and/or configurations. Furthermore, the presentinvention may take the form of a computer program product on acomputer-usable storage medium having computer-usable program codeembodied in the medium. Any suitable computer readable medium may beutilized including hard disks, CD-ROMs, optical storage devices, atransmission media such as those supporting the Internet or an intranet,or other storage devices.

Computer program code for carrying out operations of the presentinvention may be written in an object oriented programming language suchas Java®, Smalltalk or C++. However, the computer program code forcarrying out operations of the present invention may also be written inconventional procedural programming languages, such as the “C”programming language. The program code may execute entirely on theuser's computer, partly on the user's computer, as a stand-alonesoftware package, partly on the user's computer and partly on anothercomputer, local and/or remote or entirely on the other local or remotecomputer. In the latter scenario, the other local or remote computer maybe connected to the user's computer through a local area network (LAN)or a wide area network (WAN), or the connection may be made to anexternal computer (for example, through the Internet using an InternetService Provider).

The present invention is described in part below with reference toflowchart illustrations and/or block diagrams of methods, apparatus(systems) and computer program products according to embodiments of theinvention. It will be understood that each block of the flowchartillustrations and/or block diagrams, and combinations of blocks in theflowchart illustrations and/or block diagrams, can be implemented bycomputer program instructions. These computer program instructions maybe provided to a processor of a general purpose computer, specialpurpose computer, or other programmable data processing apparatus toproduce a machine, such that the instructions, which execute via theprocessor of the computer or other programmable data processingapparatus, create means for implementing the functions/acts specified inthe flowchart and/or block diagram block or blocks.

These computer program instructions may also be stored in acomputer-readable memory that can direct a computer or otherprogrammable data processing apparatus to function in a particularmanner, such that the instructions stored in the computer-readablememory produce an article of manufacture including instruction meanswhich implement the function/act specified in the flowchart and/or blockdiagram block or blocks.

The computer program instructions may also be loaded onto a computer orother programmable data processing apparatus to cause a series ofoperational steps to be performed on the computer or other programmableapparatus to produce a computer implemented process such that theinstructions which execute on the computer or other programmableapparatus provide steps for implementing the functions/acts specified inthe flowchart and/or block diagram block or blocks.

The flowcharts and block diagrams of certain of the figures hereinillustrate exemplary architecture, functionality, and operation ofpossible implementations of embodiments of the present invention. Inthis regard, each block in the flow charts or block diagrams representsa module, segment, or portion of code, which comprises one or moreexecutable instructions for implementing the specified logicalfunction(s). It should also be noted that in some alternativeimplementations, the functions noted in the blocks may occur out of theorder noted in the figures. For example, two blocks shown in successionmay in fact be executed substantially concurrently or the blocks maysometimes be executed in the reverse order or two or more blocks may becombined, depending upon the functionality involved.

Generally stated, embodiments of the systems are configured to provide asubstantially automated or semi-automated and relatively easy-to-useMRI-guided systems with defined workflow steps and interactivevisualizations. In particular embodiments, the systems define andpresent workflow with discrete steps for finding target and entrypoint(s), localizing the entry point(s) to a physical identified gridposition, guiding the alignment of the targeting canula to a plannedtrajectory, monitoring the insertion of the probe, and adjusting the X-Yposition in cases where the placement needs to be corrected. Duringsteps where specific MR scans are used, the circuit or computer modulecan display data for scan plane center and angulation to be entered atthe console. The workstation/circuit can passively or activelycommunicate with the MR scanner. The system can also be configured touse functional patient data (e.g., fiber tracks, fMRI and the like) tohelp plan or refine a target surgical site.

Embodiments of the present invention will now be described in furtherdetail below with reference to the figures. FIG. 1 illustrates an MRIguided interventional system 10 with an MRI scanner 20, a clinicianworkstation 30 with at least one circuit 30 c, at least one display 32and at least one MRI compatible interventional and/or surgical tool 50.An MRI scanner interface 40 may be used to allow communication betweenthe workstation 30 and the scanner 20. The interface 40 and/or circuit30 c may be hardware, software or a combination of same. The interface40 and/or circuit 30 c may reside partially or totally in the scanner20, partially or totally in the workstation 30, or partially or totallyin a discrete device therebetween. The system 10 can be configured torender or generate real time visualizations of the target anatomicalspace using MRI image data and predefined data of at least one surgicaltool to segment the image data and place the tool 50 in the renderedvisualization in the correct orientation and position in 3D space,anatomically registered to a patient. The tool 50 can include orcooperate with tracking, monitoring and/or interventional components.The system 10 can optionally include a reader 30 r that canelectronically read (e.g., optically such as via a bar code or otherwiseelectronically read such a via an RFID tag) a label or tag or otherindicia to confirm that the hardware is authentic or compatible toinhibit counterfeit hardware and potential misuse of the system as thesystem is configured so that certain hardware define a point ofinterface with the software or circuit 30 c. Alternatively, oradditionally, the system 10 can allow a user to manually input thetool/hardware indicia. Proper operation of the system requires that theproper hardware having the specific predefined characteristics used bythe system is used for the surgical procedure.

FIGS. 2 and 3 are schematics of embodiments of the system 10 whichillustrate that the system 10 can include a light source 100 incommunication with a camera device 110 via a fiber optic fiber bundlecable 115. FIG. 2 illustrates that the system 10 can be used forbilateral procedures. The camera device (fiberscope) 110 can have adistal lens and can be configured with a relatively small local field ofview (residing proximate the burr hole or surgical entry location) toallow a clinician to monitor the surgical entry point. The fiber-opticcamera device 110 can be mounted to the trajectory guide 50. The returnsignal is fed to an MRI compatible video camera 120 and the signal istransmitted as a video of the patient and can be shown in a display orsplit screen 32 at the workstation 30. The workstation 30 can be in acontrol room 200 and the feed from the fiber optic cable from the camera115 c can be via an RF filter 123 to inhibit signal distortion to thevideo stream shown on the display 32. A separate display or monitor canalso reside in the surgical room 210. A sterile surgical drape 118 canbe used to maintain a sterile side inside the surgical room 210 on thebore end of the magnet facing the camera 120. On example of a suitableMR compatible video camera is available from MRC Systems GmbH,Heidelberg, Germany.

The system 10 can be configured to provide workflow for a unilateral orbilateral (or even trilateral or more) procedure. Selection of theprocedure type can initiate the associated work flow presented. FIG. 4illustrates an example of a workstation control panel 30 p on displayscreen 32. The panel 30 p can illustrate a current workflow step andallow a user to go to a step directly (such as via a drop down list orselection of a workflow step in a toolbar or the like) and can bepresented adjacent different views of the intrabody trajectory andpatient anatomy. Tabs or other user-selectable features with visualfeedback on status of a step for each side can be used for steps withlaterality (e.g., left or right for bilateral procedures) to allow auser to control selection of laterality, such as left 30 a and right 30b, to complete trajectory planning for each side independently (or toallow a user to toggle back and forth while maintaining control overeach side). The display 32 can include viewer tools such as zoom, pan,width/level, magnifier, etc.

The MRI scanner 20 can include a console that has a “launch” applicationor portal for allowing communication to the circuit 30 c of theworkstation 30. The scanner console can acquire volumetric T1-weighted(post-contrast scan) data or other image data (e.g., high resolutionimage data for a specific volume) of a patient's head or other anatomy.In some embodiments, the console can push DICOM images or other suitableimage data to the workstation 30 and/or circuit 30 c. The workstation 30and/or circuit 30 c can be configured to passively wait for data to besent from the MR scanner 20 and the circuit 30 c/workstation 30 does notquery the Scanner or initiate a communication to the Scanner. In otherembodiments, a dynamic or active communication protocol between thecircuit 30 c/workstation 30 and the Scanner 20 may be used to acquireimage data and initiate or request particular scans and/or scan volumes.Also, in some embodiments, pre-DICOM, but reconstructed image data, canbe sent to the circuit 30 c/workstation 30 for processing or display. Inother embodiments, pre-reconstruction image data (e.g., substantially“raw” image data) can be sent to the circuit 30 c/workstation 30 forFourier Transform and reconstruction.

Generally described, for some unilateral scenarios, the user willproceed through a set of discrete workflow steps to load MR image data,identify a target point, identify an entry point, verify the plannedtrajectory, and align the targeting canula. A target point or region canalso be planned or refined based on real-time functional image data of apatient. The functional image data can include, but is not limited to,images of fiber tracks, images of activity in brain regions duringvocalization (e.g., reading, singing, talking), or based on physical orolefactory or sense-based stimulation, such as exposure to electrical(discomfort/shock input), heat and/or cold, light or dark, visualimages, pictures or movies, chemicals, scents, taste, and sounds or thelike) and/or using fMRI or other imaging techniques. The enhancedvisualization gives neurosurgeons a much clearer picture of the spatialrelationship of a patient's brain structures. The visualizations canserve as a trajectory guide for surgical procedures, such as brain-tumorremoval and epilepsy surgery. In some embodiments, the visualizationscan be generated using data collated from different types ofbrain-imaging methods, including conventional magnetic resonance imaging(MRI), functional MRI (fMRI), diffusion-tensor imaging (DTI) and evenhyperpolarized noble gas MRI imaging. The MRI gives details on theanatomy, fMRI or other active stimulation-based imaging protocol canprovide information on the activated areas of the brain, and DTIprovides images of the network of nerve fibers connecting differentbrain areas. The fusion of one or all of these different images and thetool information can be used to produce a 3-D display with trajectoryinformation that surgeons can manipulate.

Thus, a target location and trajectory can be planned, confirmed orrefined based in-part on functional information of the patient. Thisfunctional information can be provided in real-time visualizations ofthe patient with the trajectory guide tools for trajectory path andtarget planning, e.g., visualize a patient's fiber track structuresand/or functional information of a patient's brain for a surgeon's easeof reference. This information can also be selected or suppressed fromviews via a UI selection, such as “Show Fiber Tracks” 32F₁ and/or “ShowFunctional Output” 32F₂ (e.g., toolbar option) as shown in FIG. 4. It isnoted that the patient functional information can be shown automaticallywithout requiring a user selection or in response to a stage of aprocedure or when selecting certain steps. In addition, such informationmay be shown or selected in any appropriate display or step describedherein although not specifically described with respect to thatparticular step or screen display. Knowing where susceptible orsensitive brain regions are or where critical fiber tracks are in thepatient's brain, can allow a surgeon to plan a better, less-risky orless-intrusive trajectory and/or allow a surgeon to more precisely reacha desired target site and/or more precisely place a device and/ordeliver a planned therapy, e.g., implant a stimulation lead, ablatetissue and/or treat a tumor site and/or excise a tumor, deliver a geneand/or stem cell therapy and the like.

To align the targeting canula, scan volumes can be defined by the systembased on known dimensions of the canula, such as a canula length aposition of a proximal or distal marker on the canula, and angulationand lateral (X-Y) pivot limit. In particular embodiments, the user canthen gradually advance a probe and a peel away sheath (that isconfigured to guide an interventional device to a desired location alongthe defined trajectory) and acquire images to check for hemorrhage andto verify the trajectory and/or avoid functionally sensitive structure.When the probe has been advanced to the target point, high-resolutionconfirmation images can be obtained to verify the tip location relativeto the planned location. If actual placement is unacceptable, the probecan be withdrawn. At that point, either the X-Y placement can beadjusted appropriately (e.g., by moving a platform or stage an amount tocause the desired adjustment) or a trajectory angulation can bere-planned and a second attempt can be made.

For some bilateral scenarios, the above steps can be repeated for bothleft and right sides, with the additional goal that the patient shouldnot be moved into or out of the scanner. To satisfy that goal,trajectory planning should be completed for both sides prior to removingthe patient from the scanner. Also, burring and frame attachment (themember that holds the trajectory guide to the patient's head) should becompleted for both sides prior to moving the patient back into thescanner to promote speed of the procedure.

The system 10 can be configured with a hardware interface that providesa network connection, e.g., a standard TCP/IP over Ethernet networkconnection, to provide access to MR scanner 20, such as the DICOMserver. The workstation 30 can provide a DICOM C-STORE storage classprovider. The scanner console can be configured to be able to pushimages to the workstation 30 and the workstation 30 can be configured todirectly or indirectly receive DICOM MR image data pushed from an MRScanner console. Alternatively, as noted above, the system can beconfigured with an interface that allows for a dynamic and interactivecommunication with the Scanner 20 and can obtain image data in otherformats and stages (e.g., pre-DICOM reconstructed or raw image data).

As noted above, the systems 10 are configured so that hardware, e.g.,one or more specific surgical tools, constitute a point of interfacewith the system (software or computer programs) because the circuit 30 cis configured with predefined tool data that recognizes physicalcharacteristics of specific tool hardware.

As shown in FIG. 5, to assure proper operation, the system 10 can beconfigured to require entry of a valid identifier and/or revisioncontrolled/based part number to validate that the hardware planned foruse is appropriate for use in the system 10 (or at least that version ofthe system). Thus, a reader 30 r associated with the workstation 30 canbe configured to read a single “group” identifier 66 that can be placedon the kit package or provided with the kit 10 k and/or the reader canbe configured to read each tool that has predefined characteristics toconfirm the appropriate part and version is in the kit. Alternatively,or additionally, the system 10 can allow a user to manually input thetool/hardware identifier data (e.g., hardware version and/or partnumber) into a UI associated with the circuit 30 c. The workstation 30can include a look-up chart of a correlation table 31 that confirms thecorrect hardware is in the kit 10 k or otherwise provided for use. Thus,the workstation 30 can be configured with a user interface 32I (shown asa Tool Version Identifier Panel) that requires a user to electronicallyor manually enter the identifier 66 and/or to acknowledge compliancewith the tool-specific operation of the system 10. It is envisioned thatthe circuit 30 c can be configured with updates and backwardcompatibility for future controlled changes to the specific tools and/orwith the ability to use different module versions of the systemaccording to the version of the tool or tools then in use at thesurgical site.

To inhibit the use of counterfeit hardware with the system 10, theidentifier may include indicia that can be keyed to a particularauthorized use site and/or authorized user. The system may be configuredto require a user to certify that the hardware is OEM hardware orauthorized hardware to be able to receive an electronic key to be ableto activate the system. A user may be required to contact the OEM orother authorized party to obtain an electronic key or identifier toallow use of the hardware with the system 10.

As shown in FIG. 5, in some embodiments, the system is programmaticallyconfigured to recognize defined physical characteristics of differenttools. Those tools that can be provided as a kit 10 k (typically asingle-use disposable hardware) or in other groups or sub-groups or evenindividually, typically provided in suitable sterile packaging. Thetools can include at least one marking grid 50 g (also referred to as agrid patch), a targeting canula 60 with a distal marker 60 m and anopposing proximal portion of the canula 60 p. The targeting canula 60can include an open center lumen or passage 61 (FIG. 8). The distalmaker 60 m typically includes a substantially spherical fluid filledcomponent 65 (FIG. 8). The proximal portion of the canula 60 p caninclude a marker, but is typically identified in the image data based,at least in-part) on the distal maker 60 m and its known distance andorientation with respect thereto based on the physical characteristicsof the targeting canula 60. Still referring to FIG. 5, the system 10 canalso include a trajectory guide 50 t with a plurality of MRI visibleframe fiducial markers 50 fm around a base 50 b thereof. The system 10may also include a stylet that can communicate with a peel-away sheath50 s and an imaging probe 50 a (that provides an intrabody receiveantenna that can be slidably introduced via the passage of the targetingcanula 60). Certain components of the kit may be replaced or omitteddepending on the desired procedure. Certain components can be providedin duplicate for bilateral procedures. As shown in FIG. 5, a therapydelivery device 52 may optionally be provided, also with an identifiersuch as a label or tag 66. The device 52 can be configured to flowablyintroduce and/or inject a desired therapy (e.g., gene therapy orstem-cell or other therapy type) or obtain a biopsy and the like.

FIGS. 6A-6C, and 7-10 illustrate the trajectory guide 50 t with thetargeting canula 60 and various features described above. FIG. 6Aillustrates a trajectory guide 50 t and targeting canula 60 in positionon a patient with trajectory guide actuators 151 and respective actuatorcables 150 a-150 d (providing X-Y adjustment and pitch and rolladjustment) in communication with a trajectory adjustment controller400. The frame 150 f can include control arcs 152 (FIGS. 7, 10) thatcooperate with a platform 153 (FIG. 7) to provide pitch and rolladjustments. The platform 153 can allow for X-Y adjustments of thetrajectory. For additional discussion of suitable trajectory guides,see, U.S. application Ser. No. 12/134,412, and co-pending, co-assignedU.S. patent application Ser. No. 12/236,950, the contents of which arehereby incorporated by reference as if recited in full herein.

FIGS. 6B and 6C illustrate examples of a depth stop 210 cooperating withan elongate member 212 such as, for example, a stimulation or ablationlead, a diagnostic and/or imaging probe, a removable sheath and/or othertherapy or diagnostic device inserted and secured therein asillustrated. The illustrated depth stop 210 has a generally cylindricalconfiguration with opposite proximal and distal ends 210 a, 210 b and isadapted to be removably secured within the proximal end of the tubulartrajectory guide member 50 t (FIG. 6A). The depth stop 210 is configuredto limit a distance that the member 212 extends into the body of apatient when the depth stop is inserted within the tubular member 50 tor 60. The member 212 can include visual indicia of insertion depth 215to allow a user to visually attach the stop 210 at the appropriatelocation that provides the desired insertion depth.

As shown in FIGS. 6C and 6D, in some embodiments, the depth stop 210 isattached to a peel-away sheath 212 s (see also probe 50 s, FIG. 5) andcan be configured to receive and guide an elongated interventionaldevice, such as a stylet or imaging probe, therethrough. As shown inFIGS. 6C and 6D, the sheath 212 s can include opposing tabs that, whenpulled apart, cause the sheath to peel away for removal from thetargeting canula 60. In other embodiments, the depth stop 210 can beattached to a stimulation lead to allow for a defined insertion depth(see, e.g., FIG. 38 below) or other device where insertion depth controlis desired.

As shown in FIG. 7, the targeting canula 60 can be attached to thetrajectory guide 50 t. The targeting canula 60 can include a throughpassage 61. The distal end of the targeting canula 60 has a fiducialmarker 60 m, shown as a substantially spherical or round (cross-section)marker shape. The proximal end 60 p can be configured with a fluidfilled channel 68 concentric with the passage 61 that can define acylindrical fiducial marker. Along the axis of the canula 60, there isthe lumen or passage 61 through which another device can be slidablyintroduced and/or withdrawn, e.g., a stylet 50 s, imaging probe 50 a,therapy delivery or diagnostic device 52 (FIG. 5) and DBS stimulationleads for implantation, can be advanced into the brain.

FIG. 11A illustrates an example of a grid patch 50 g with physicalcharacteristics that are predefined and available to or in the circuit30 c (e.g., software application). FIG. 11B illustrates that the gridcan allow for precise correlation of logical points in an MR volume withthe physical patient. The system 10 can be configured to generate a 3-Dvolumetric view on the display 32 with overlays to show the grid 50 gand an entry point and grid coordinates (and optionally grid edges)allowing a burr hole mark to be made on a skull at the desired plannedentry point.

FIGS. 12A-12E illustrate a series of operations that can be carried outfor the grid 50 g segmentation. Some or all of these operations may becarried out behind the scene (e.g., not actually displayed). FIG. 12Aillustrates an example of a histogram. FIG. 12B is an example of aninitial distance image. FIG. 12C is an image of a result of searchingfor the grid in the initial distance image. FIG. 12D illustrates theresult of searching for the grid in the optimal distance image, withsmall step sizes. FIG. 12E illustrates the result of spatially deformingthe grid to fit the head surface and interpolating the grid cells tofind the vertices.

With reference to FIG. 12A, the amplitude of the background noise in theinput image stack can be estimated. To do so, a histogram of the stackcan be constructed. The first negative maximum of the slope of thehistogram can be located. The first peak to the left of this maximum canbe located (this can be termed the “noise peak”). The difference betweenthe noise peak and the first negative maximum of the slope canapproximate the standard deviation of the noise. The noise threshold canbe obtained using the following Equation (1).(noise threshold)=(noise peak)+4*(noise standard deviation)  EQUATION(1)

The above can be considered as a first step in the grid segmentation ofthe image data. Steps 2-5 can be carried out as described below to placethe grid in position and deform to curvature of the skull for the gridsegmentation.

-   -   2. Estimate the “optimal view direction” for the grid. This is        defined as the vector from the grid center to the midpoint of        the AC-PC line:    -   a. Construct an initial distance image as shown in FIG. 12B        starting from a rough estimate of the optimal view direction:        -   i. Create an image plane that is perpendicular to the            estimated view direction, and outside of the head volume.        -   ii. For each pixel in the image plane, record its distance            to the first voxel in the image volume that is above the            noise threshold.    -   b. Find the grid cells in the distance image:        -   i. The grid cells are “bumps” on the head surface, so they            appear as local minima in the distance image. This            characteristic is enhanced by applying a            Laplacian-of-Gaussian operator to the distance image.        -   ii. For each location in the image, place a virtual grid            (whose dimensions match those of the physical grid), at            several orientations. Compute a score by tallying 1 point            for each virtual grid cell that lands on one of the image            minima. The highest score corresponds to the location and            orientation of the grid in the distance image.    -   c. The center of the grid so obtained gives a new estimate of        the optimal view direction. This estimate is used as a starting        point of a new iteration of steps 2a, and 2b, in order to refine        the estimate.    -   3. Find the grid using the optimal view direction:    -   a. Construct a distance-image as described in step 2a, but using        the optimal view direction obtained in step 2.    -   b. Find the grid in the new distance image, as described in 2b.    -   c. Refine the grid position and orientation by repeating the        search procedure of 2b, but search only in a small region around        the known approximate location, with very fine step-sizes (see,        FIG. 12D).    -   4. Deform the grid to the shape of the head:    -   a. Up to this point, the grid has been taken to be planar.    -   b. Fit the grid cell locations in the distance image to a cubic        surface using a robust regression algorithm, and snap each grid        cell from step 3 to this surface. (This is to avoid producing a        very irregular grid surface due to noise and low resolution in        the distance image.)        -   Note that, in general, it is not possible to maintain equal            distances between the grid cells when they are snapped to an            arbitrary curved surface. Therefore an algorithm which            simulates the behavior of the physical grid patch is used to            minimize the amount of stretching and bending during the            deformation.    -   5. Interpolate between the grid cells to compute the grid        vertices. FIG. 12E illustrates a deformation result.

FIGS. 13A-13C illustrate images associated with a series of operationsthat can be carried out for frame marker segmentation. FIGS. 9 and 10illustrate an example of a frame 50 f with fiducial markers 50 fmcircumferentially spaced apart around a center “cp” and around a spacefor the burr hole with two of the markers 50 fm ₁, 50 fm ₂ closertogether than a third 50 fm ₃ (FIG. 10). Different arrangements,configurations or numbers of fiducial makers as well as differentlocations on the frame 50 f and/or guide 50 t may be used and the framesegmentation can be altered accordingly.

Some or all of these operations illustrated in or described with respectto FIGS. 13A-C may be carried out behind the scene (e.g., not actuallydisplayed). FIG. 13A illustrates an exemplary histogram with a noiseregion. FIG. 13B illustrates a cross-section of an imaged frame-marker.FIG. 13C illustrates a result of fitting a circle to the edge mask shownin FIG. 13B. The frame marker segmentation can define the orientation ofthe trajectory guide on the patient that can be correlated to mechanicaloutput to cause the trajectory guide 50 t to translate to provide adesired trajectory, e.g., rotations and/or direction left, right,counterclockwise or clockwise or other translation for moving theactuators to change pitch and/or roll (or X-Y location).

With reference to FIG. 13A, the amplitude of the background noise in theinput image stack can be estimated. To do so, a histogram of the stackcan be constructed, the first negative maximum of the slope of thehistogram can be located, the first peak to the left of this maximum canbe located (this is the noise peak). The difference between the noisepeak and the first negative maximum of the slope can approximate thestandard deviation of the noise. The noise threshold can be obtainedusing the Equation (1) above. Again, this can be considered a first stepin segmentation. Then, Steps 2-6 can be carried out with respect to theframe marker segmentation based on fit of an expected fiducial geometryto the observed fiducial positions because the fiducial markers arearranged with a fixed geometric relationship inside the volume.

-   -   2. Use a region-growing algorithm to find all “clumps” of pixels        that are above the noise threshold.    -   3. Discard all clumps whose volumes are far from the known        frame-marker volume.    -   4. Discard all clumps whose bounding-box dimension are far from        the known bounding-box dimensions of the frame-markers.    -   5. Among the remaining clumps, look for triplets whose spatial        arrangement matches the known spatial arrangement of the        frame-markers of the trajectory base 50 b (i.e., the centroids        of the clumps should form a triangle (e.g., an isosceles        triangle) of known dimensions.)

At this point, if the number of clumps found for each frame (wherebilateral procedures are used, there are two frames) is not exactly 3,then the segmentation is deemed to have failed.

-   -   6. For each triplet of markers, refine the marker locations:    -   a. Extract a 2D image of each marker by reformatting the stack        onto the plane defined by the 3 marker centroids.    -   b. Compute the Canny edge mask of each 2D marker image.    -   c. Fit a circle to the Canny edge mask. The circle diameter is        set equal to the diameter of the physical frame markers. The fit        is performed by moving the circle until its overlap with the        edge mask is maximized. The center of the fit circle is taken to        be the location of the frame-marker's center.

In some embodiments, circuit 30 c can be configured so that the programapplication can have distinct ordered workflow steps that are organizedinto logical groups based on major divisions in the clinical workflow asshown in Table 1. A user may return to previous workflow steps ifdesired. Subsequent workflow steps may be non-interactive if requisitesteps have not been completed. The major workflow groups and steps caninclude the following features or steps in the general workflow steps of“start”, “plan entry”, “plan target”, “navigate”, and “refine,”ultimately leading to delivering the therapy (here placing thestimulation lead).

TABLE 1 EXEMPLARY CLINICAL WORKFLOW GROUPS/STEPS Group Step DescriptionStart Start Set overall procedure parameters (Optionally confirmhardware compatibility) Plan ACPC Acquire a volume and determine AC, PC,and Entry MSP points Target Define initial target point(s) for entryplanning Trajectory Explore potential trajectories to determine entrypoint(s) Grid Locate physical entry point via fiducial grid. Plan ACPCWith hole burred and frame attached, acquire a Target volume anddetermine revised AC, PC, and MSP points. Target Acquire high-resolutionslabs (e.g., T2 slabs) to determine target positions in new volume.Trajectory Review final planned trajectory prior to starting procedure.Navigate Initiate Acquire slabs to locate initial position of canula.Alignment Dynamically re-acquire scan showing position of top of canula.With each update show projected target position to determine whenalignment is correct. Insertion Acquire slabs as probe is inserted intobrain. Verify that probe is following planned trajectory. Refine TargetAcquire images with probes in place. Review position and redefine targetif necessary. Adjust XY Dynamically re-acquire scan showing position ofOffset bottom of canula. With each update show proj- ected targetposition to determine when offset is correct. Insertion Acquire slabs asprobe is inserted into brain. Verify that probe is following plannedtrajectory. Lead Once probe position is finalized, prompt user toPlacement place DBS leads or other device. Admin Admin Reporting andArchive functionality.

TABLES 2A-2P provide additional examples of some exemplary operationsthat may be associated with exemplary workflow steps according to someembodiments of the present invention.

TABLE 2A Workflow Group Start Step Description The start step canprovide UI (User Interface) for selecting procedure laterally. The startstep can provide UI for selecting target: STN, Gpi, or Custom The startstep can provide UI for specifying the scanner bore diameter or scannertype that defines the size. The start step can provide UI for enteringhardware identifier data (e.g., version code) from the disposablehardware kit. If the version does not match the version supported by thesoftware, an error can be shown, and the application can remaindisabled.

TABLE 2B Plan Entry - AC-PC Step Description While data is being sent tothe application, the UI can be disabled. Given a 3D MR series of a wholehuman head, the application can automatically identify the AC, PC, andMSP points. The application can display reformatted coronal, sagittal,and axial views aligned to the current AC, PC, and MSP points. AC, PC,and MSP points can be editable in any MPR view in this step. On changingthese points, the views can update to realign to the new ACPC coordinatesystem. If a new series is sent while in this step, it will replace theexisting series and clear all annotations. While detecting the AC, PC,and MSP points, the UI can be disabled. If additional data belonging tothe current 3D MR series is sent, the AC, PC, and MSP points can bere-calculated automatically.

The AC, PC and MSP locations can be identified in any suitable manner.In some embodiments, the AC-PC step can have an automatic, electronicAC, PC MSP Identification Library. The AC, PC and MSP anatomicallandmarks define an AC-PC coordinate system, e.g., a Talairach-Tournouxcoordination system that can be useful for surgical planning. Thislibrary can be used to automatically identify the location of thelandmarks. It can be provided as a dynamic linked library that a hostapplication can interface through a set of Application ProgrammingInterface (API) on Microsoft Windows®. This library can receive a stackof MR brain images and fully automatically locates the AC, PC and MSP.The success rate and accuracy can be optimized, and typically it takes afew seconds for the processing. The output is returned as 3D coordinatesfor AC and PC, and a third point that defines the MSP. This library ispurely computation and is typically UI-less. This library can fit aknown brain atlas to the MR brain dataset. The utility can be availablein form of a dynamic linked library that a host application caninterface through a set of Application Programming Interface (API) onMicrosoft Windows®. The input to this library can contain the MR braindataset and can communicate with applications or other servers thatinclude a brain atlas or include a brain atlas (e.g., have an integratedbrain atlas). The design can be independent of any particular atlas; butone suitable atlas is the Cerefy® atlas of brain anatomy (note:typically not included in the library). The library can be configured toperform segmentation of the brain and identify certain landmarks. Theatlas can then be fitted in 3D to the dataset based on piecewise affinetransformation. The output can be a list of vertices of the interestedstructures.

In some embodiments, the mid-sagittal plane (MSP) is approximated usingseveral extracted axial slices from the lower part of the input volume,e.g., about 15 equally spaced slices. A brightness equalization can beapplied to each slice and an edge mask from each slice can be createdusing a Canny algorithm A symmetry axis can be found for each edge maskand identify the actual symmetry axis based on an iterative review andranking or scoring of tentative symmetry axes. The ranking/scoring cambe based on whether a point on the Canny mask, reflected through thesymmetry axis lands on the Canny mask (if so, this axes is scored forthat slice). An active appearance model (AAM) can be applied to a brainstem in a reformatted input stack with the defined MSP to identify theAC and PC points.

The MSP plane estimate can be refined as well as the AC and PC points.The MSP plane estimate can be refined using a cropped image with a smallregion that surrounds a portion of the brain ventricle and an edge maskusing a Canny algorithm. The symmetry axis on this edge mask if foundfollowing the procedure described above. The AC and PC points areestimated as noted above using the refined MSP and brightness peaks in asmall region (e.g., 6×6 mm) around the estimate are searched. Thelargest peak is the AC point. The PC point can be refined using the PCestimate above and the refined MSP. A Canny edge map of the MSP imagecan be computed. Again, a small region (e.g., about 6 mm×6 mm) can besearched for a point that lies on a Canny edge and for which the imagegradient is most nearly parallel to the AC-PC direction. The point ismoved about 1 mm along the AC-PC direction, towards PC. The largestintensity peak in the direction perpendicular to AC-PC is taken to bethe PC point.

TABLE 2C Plan Entry - Target Step Description The application canprovide the ability to save position coordinates as default values forthe STN and Gpi targets. Initially these default values are set to 0, 0,0. Saved values can appear as the default for subsequent proceduresusing that target. The application can also provide custom targets forwhich no default coordinate is supplied. When this option is selected,the user will be able to define a set of custom-named targets associatedwith a single entry point. The application can display anatomic coronal,sagittal, and axial views. Target points can be editable in any MPR viewin this step. The application can provide functionality to automaticallyregister a brain atlas to the patient volume and generate outlines ofstructures associated with the selected target and display correspondingcontours on the MPR views. The application can provide interface tomanually scale and offset the brain atlas registration to better matchobserved patient anatomy.

TABLE 2D Plan Entry - Trajectory Step Description For each given targetpoint, the user can specify the corresponding entry point. Theapplication can display oblique reformatted coronal, sagittal, and axialviews aligned to the proposed trajectory. Entry points can be editableon either the oblique sagittal or coronal viewports in this step. Theoblique axial view can provide cine functionality to animate afly-through along the trajectory. The application can also provide ananatomical axial view. The respective positions of the anatomical andoblique axial views can be represented by lines on the oblique sagittaland coronal views. When multiple targets (custom targets) have beendefined for an entry point, the application can provide means to selectthe current target to display. Edits to the entry point will change theentry point for all associated targets. If the user attempts to set thetrajectory such that the probe could not be inserted without strikingthe bore an error can be shown and the trajectory will not be set. Thismakes use of the bore size typically entered on the Start step. Theapplication can provide means to define named trajectories within thestep. Trajectories from the list of named trajectories may be selectedfor display in the step. If the user moves the entry point off the edgeof the grid, warning text will be shown.

TABLE 2E Plan Entry - Grid Step Description The application can displaya volumetric 3D view showing the planning volume. For a bilateralprocedure 2 such views can be shown, the left side in the left viewport,the right in the right viewport. The application can optionally displaythe grid coordinates of the marking grid. The application can optionallydisplay overlay graphics to visually identify edges and positions withingrid squares. On each view, the application can display thecorresponding entry point The application can automatically align the 3Dviews such that the user's point of view is looking along the trajectoryfrom the entry towards the target. In the case of multiple customtargets, the trajectory to the first target can be used. The applicationcan set the visualization parameters of the volume such that the griditself is visible to the user. The initial zoom level can ensure thatthe entire head is visible.

At this point, holes have been burred at the entry points and thetrajectory guides 50 t have been attached. NOTE: Because the patient hasbeen moved, points defined in the previous image coordinate system mayno longer be valid. Also, brain shift may occur at this point.

TABLE 2F Plan Target - AC-PC Step Description The Plan Target AC-PC stepcan look and function the same as in the planning AC-PC step. However,data received in this step can be stored as the replanning volume. TheAC, PC, and MSP annotations and the resultant transformation derivedfrom the replanning volume can be kept distinct from those determined inthe planning AC-PC step.

TABLE 2G Plan Target - Target Step Description The Plan Target Step canfunction the same as in the planning step but with additionalfunctionality to support slab data fusion. The Plan Target Step canaccept DICOM slab data. While receiving slab data, the UI can bedisabled and a message should be shown to indicate that a data transferis in progress. The Plan Target Step can provide a thumbnail bar thatlists series in their order of acquisition. Selecting a series in thethumbnail bar will cause it to appear fused with the re-planning volume.Selecting the Plan Target volume can cause it to be displayed by itself.Fused data can appear in the viewports along with the - plan targetvolume images and will be positioned and scaled to exactly coincide withthe position and scale of the plan target volume. The control panel cancontain a slider that controls the relative intensity of the two seriesin the blended viewports. The step can display scan plane parameters foran anatomical axial slab through the current target.

TABLE 2H Plan Target - Trajectory Review Step Requirement descriptionThe Plan Target Trajectory Review Step can function the same as thePlanning Trajectory review step with only the following exceptions: Slabfusion support Segment out the pivot point from frame markers Use pivotpoint position as a fixed entry point (not editable) The Plan TargetTrajectory Step can accept DICOM slab data. While receiving slab data,the UI can be disabled. The Plan Target Trajectory Review Step canprovide a thumbnail bar that lists series in their order of acquisition.Selecting a series in the thumbnail bar will cause it to appear fusedwith the re-planning volume. Selecting the re-planning volume can causeit to be displayed by itself. Fused data will appear in the viewportsalong with the volume images and will be positioned and scaled toexactly coincide with the position and scale of the re- planning volume.The control panel can contain a slider that controls the relativeintensity of each series in the blended viewports. If for any reason thesoftware is unable to identify the frame markers to find the pivotpoint, a warning can be displayed. The step can display scan planeparameters for: an oblique sagittal slab along the trajectory an obliquecoronal slab along the trajectory The step can display the trajectoryangles relative to the anatomical coronal and sagittal planes.

TABLE 2I Navigate - Initiate Description The step can prompt the user toacquire a small high- resolution slab through the proximal canula at adistance such that it will show a cross-section of the proximal canulaeven at maximum angulation and maximum offset. The slab can have aminimum of 4 slices. (Example: given a canula 83 mm long, a maximumangulation of +/−35 degrees, and a maximum offset of 4 mm, then a scanplane 65 mm up from the distal canula marker will be sufficient toensure that the canula is visible in the slab.) The application can alsoprompt the user to acquire a small high resolution slab scan with thefollowing attributes: plane aligned to the plane of the frame markers(this can be based on the frame segmentation that was done for thetrajectory review step) plane center is positioned at the mechanicalcenter of rotation slab thickness is large enough to include all of thedistal canula marker even under maximum angulation and offset (Example:given a maximum angulation +/−35 degrees, a maximum offset of 4 mm, anddistal canula marker size of 7.1 mm, the total thickness required wouldbe 11.6 mm, so any larger value may be used, say 13 mm) slice spacingcan be about 1 mm The application can identify the positions of theproximal and distal canula. Using the detected positions of the framemarkers in the plan target volume, the application can compare theobserved position of the distal canula with the mechanical center ofrotation. Since a locking pin may be used to ensure that there is nooffset, values above a low threshold can cause a warning to bedisplayed. (Example warning text: “Distal canula marker not found atexpected location. Verify that canula is locked in ‘down’ position andreacquire distal canula scan.”) If no pivot point marker can beidentified, the user will be prompted to verify that the canula islocked in the ‘down’ position and re-acquire the slab scan. The step canprovide 3 MPR viewports in which to display the acquired slabs. Theseviewports will be oriented such that their base planes are aligned tothe detected canula axis. The step can provide a thumbnail bar to allowthe user to select which acquired slab to display.

TABLE 2J Navigate - Alignment Description The application can prompt foran alignment scan with the following attributes: scan plane isperpendicular to planned trajectory scan plane is centered around thetrajectory scan plane position is set such that a cross- section of theproximal canula will be shown even at maximum angulation and maximumoffset. a single 2D image can be acquired The application can display ananatomical axial view through the currently selected target. The usermay opt to switch the display to show a trajectory-axial view. Onreceiving a 2D image of the top of the canula, the application canautomatically identify the position of the top of the canula in 3Dspace. Using this position and, previously-determined pivot point, andthe previously- determine offset, the application can draw an annotationrepresenting the intersection of the current trajectory with the imageplane containing the planned target. This step can display lines fromthe current projected target to the planned target that indicate thetrack the projected target would travel if the pitch and roll wheelswere turned independently. These lines can be colored to match colors onthe control wheels for pitch and roll respectively. A tool-tip (e.g.,pop-up) can provide text to describe the suggested action. (For example:“Turn Roll knob to the Left”) On re-calculating the projected targetpoint, an error value can indicate the in-plane linear distance betweenthe projected target point and the planned target point on thecurrently-displayed plane. Images that are not oriented correctly to therequested scan plane can result in a warning. In this case, annotationsand error measurements may not be displayed. Images in which thetargeting canula cannot be identified can result in a warning.Annotations and error measurements may not be displayed. When multipletargets have been defined for an entry point, the application canprovide means to select the current trajectory to display. When drawingthe target and the current projection of the canula path, theannotations can be drawn to match the physical size of the probediameter.

TABLE 2K Navigate - Insertion Description The application can provide adepth value to set on the depth stop prior to insertion. The applicationcan prompt with scan parameters for oblique coronal and sagittal planesaligned to the trajectory. Also for an oblique axial perpendicular tothe trajectory. On receiving coronal or sagittal images, the applicationcan display an overlay graphic indicating the planned trajectory. Themost recent coronal and sagittal images can appear together in a 1 × 2display. On receiving a trajectory axial scan perpendicular to thetrajectory, the application can segment out the cross- sections of theprobe to determine the actual path being followed by the probe. Onreceiving a trajectory axial scan perpendicular to the trajectory, theapplication can display two viewports containing: the axial stack withgraphic overlays showing the detected path of the probe on each image ananatomic axial view through the target showing the planned target andthe target projected from the detected path of the probe. An error valuecan show the distance between the current projected target and theplanned target. If multiple trajectories have been defined for a singleentry, the application can display the trajectory that is currentlyaligned during insertion. On entering the insertion step, theapplication can instruct the user to ensure that if they are using animaging probe that it is connected to the scanner as an internal coil.Failure to do so could cause heating of the coil and injury to thepatient. The user must explicitly click a button to acknowledge thatthey understand the warning.

TABLE 2L Refine - Target Description The step can prompt for either i) ahigh-resolution 2D image to be acquired using the imaging probe or ii) ahigh-resolution slab through the target area. The associated scan planeparameters can specify a trajectory axial image centered on the target.The application can provide means to identify the tip of the probe (orstylet), and provide an error value for the linear distance from theprobe to the planned target point in the axial anatomic plane. Theapplication can provide UI to set an updated target point. The user mayopt to proceed to the X-Y Adjustment step, return to Alignment to alignto another target, or advance to the Admin step. On accepting thecurrent position, the user can be shown a warning not to scan once theMR-incompatible DBS leads (if they are incompatible or potentiallyincompatible) have been placed. For bilateral cases, the user proceedsto complete the insertion of the probe on both sides before placing theleads. The message can indicate that scanning with MR-incompatible leadsmay result in serious injury or death. If the user modifies a targetpoint, the step can prompt the user to confirm removal of the offsetlocking pin from the targeting frame before going on to the next step.

In the event that the placement is not acceptable, the user may opt toproceed to the X-Y Adjustment workflow step.

TABLE 2M Refine - Adjust X-Y Offset Description The X-Y Adjustment stepcan display the current target and projected point as annotations to theimage data that was acquired during the Target Refinement step. Thisstep can prompt the user to acquire 2D images with scan plane parameterssuch that the image lies perpendicular to the trajectory and through thepivot point. On receiving a 2D image through the pivot point, the stepcan calculate the current projected target and display an annotation onthe 2D image from the imaging probe. This step can display lines fromthe current projected target to the revised target that indicate thetrack the projected target would travel if the X and Y offset wheelswere turned independently. The lines can be colored to match colors onthe control wheels for X and Y offset respectively. A tool-tip (e.g.,pop-up) can provide text to describe the necessary action. (For example:“Turn X-offset knob to the Left”) This step can display an annotationindicating the location of the original planned target. When drawing thetarget and the current projection of the canula path, the annotationscan be drawn to match the physical size of the probe diameter.

TABLE 2N Refine - Insertion Description After completing the X-YAdjustment, the application can provide a workflow step to guideinsertion. This is substantially the same as the first instance of theInsertion step above.

TABLE 2O Refine - Lead Placement Description After probe has been placed(or both probes for bilateral case) and position has been accepted byuser, the user may proceed to the lead placement step. This step canprovide the user with the depth values for the placement of the leads.This step may advise the user that once leads have been placed scans maynot be performed because heating in the leads could cause injury ordeath to the patient.

TABLE 2P Admin Step Description The step can provide means to archivedata relating to the procedure. This includes: trajectory planning datalog files with case data image data The step can provide functionalityto automatically generate a report documenting the performed procedure.This report can include: patient information AC, PC, and MSP points inMR space (Both detected and user-specified, if user modified.) Plannedand corrected targets in both MR and ACPC space elapsed time for theprocedure physician case notes (optional) any screenshots taken duringthe procedure An anonymous version of the report can also be generatedautomatically with the patient name and id removed. The step can provideUI whereby the user can: selected a target specify a position in MRcoordinates representing the lead tip define a set of offsets indicatingthe electrode offsets from the lead tip For each offset value, the stepcan find provide the ACPC coordinate that corresponds to a point offsetfrom the tip position back along the trajectory of the lead. Thesevalues correspond to the electrode positions in ACPC space. These valuesmay be added to a patient report. The Admin step can include a button toshut down the application on completion of the procedure. The user maynot be allowed to otherwise close the application. The application canhave a configuration value to specify whether all patient data is to becleared from the system on shut down.Again, it is noted that functional patient data can be obtained inreal-time and provided to the circuit 30 c/workstation 30 on the display32 with the visualizations of the patient anatomy to help in refining orplanning a trajectory and/or target location for a surgical procedure.

When displaying images or visualizations that were created with theimaging probe 50 a (FIG. 5, where used), the circuit 30 c mayelectronically apply a (sigma) correction to correct for a ‘volcano’ or‘halo’ shaped intensity distortion. That is, in some particularembodiments, the imaging probe antenna or coil may introduce adistortion in the images that are created with it that may be describedas a bright halo around the probe itself where it appears in the image.Thus, when images from the imaging probe have such a feature, thecircuit 30 c can be configured to electronically automatically apply acorrection to cancel out the halo (or at least reduce it). This featurewill only affect the small field, high-resolution images that arecreated via the imaging probe itself. Images obtained using the mainhead coil do not typically have such a distortion.

Referring to FIG. 14A, the circuit 30 c can be configured with a singlecontrol tool bar 30 t that is displayed on the display 32 that allowsthe user to select what group and step to go to and also shows whichgroups and steps have been completed. FIG. 14B shows an example of theworkflow control tool bar 30 t with the “Plan Entry” group selected, andthe “Define Target” enlarged as the current step. The tool bar 30 t caninclude a color border 130 that can be used to partially or totallysurround a button 130 b to illustrate completion of a step. Forbilateral procedures, the border can be color enhanced on one side whena task for that side is completed, e.g., on the left side when the lefttarget is complete in the Define Target step.

As the user works through the procedure, certain clinical information isstored to be incorporated into a procedure report that may be reviewedat the end of the procedure and/or archived as a patient record. Thecircuit 30 c can be configured to provide a user interface (UI) 30I thatprovides viewing tools, such as one or more of the following features.

-   -   Draw measurement lines    -   Pan view    -   Zoom, Zoom All, Zoom to Region, Zoom to Point    -   Magnifying glass    -   Show/Hide Annotations    -   Show/Hide Crosshairs    -   Drag views between panels    -   Resize view panels    -   Maximize view to a 1×1 display    -   Save screen capture (can be added to the report)    -   Reset view settings to default

FIG. 15 is a screen shot of an exemplary UI 30I for the Start Groupwhich may conveniently be configured as a one-screen input to setoverall procedure parameters such as laterality, target type and MRScanner bore size (recognizing that open bore MRI Scanner systems mayalso be used). Instead of bore size, a drop-down list can be providedthat allows a user to select a manufacturer and type of MR Scanner inuse that provides the associated bore size. Of course, the system 10 canbe configured as an MR Scanner-specific system or the MR Scanners of thefuture may have a standard bore size or be configured so that bore sizeis not a constraint and this information may not be required. As shown,the UI 30I can also include an input 32I that requires entry of hardwareidentifier data 66, shown as disposable kit version input, as discussedabove with respect to FIG. 5. In order to assure hardware and softwarecompatibility and/or proper operation, if the identifier data 66 doesnot match, the system 10 can be configured to not allow a user toproceed to a next step or may prompt the user for other key codes.

Bore size is used in the step Plan Entry/Trajectory. If the user selectsa trajectory such that the probe cannot be inserted into the canula 60because it will not physically fit inside the scanner bore, a warning isgenerated (visual on the display 32 and/or audible). See PlanEntry/Trajectory step above.

FIG. 16 is a screen shot associated with an exemplary UI 30I with a PlanEntry workflow group for a Define Target step (shown as left STN)illustrating the toolbar 30 t and cross hair location data with defaultlandmarks with patient image data. This step can be used to establishthe AC PC coordinate system. On receiving a whole-head volume, the stepcan automatically find candidates for these points. The user is toreview and correct these points if necessary. The user can eitherposition the crosshairs at a point and “click” the ‘Set’ button to setthe desired annotation, or they can drag an existing annotation aroundon the screen. Once points are defined, view planes can automaticallyreformat to align them to the ACPC coordinate system to show theanatomical planes: Coronal, Sagittal, and Axial. Any subsequent edit tothe landmarks can cause the view planes to instantly re-align to match.

FIG. 17 illustrates another exemplary screen shot for a Define Targetstep which is used to set target points so that the trajectories throughpotential entry points can be investigated in the next step. The usermay opt to overlay the outlines from a standard brain atlas over thepatient anatomy for comparison purposes which may b provided in colorwith different colors for different structures. FIG. 17 shows the playentry of the Define Target step with no atlas. FIG. 18 illustrates theUI with an atlas showing a target outline in three orthogonal views andFIG. 19 illustrates an atlas showing structures in a 1×1 layout. Theview planes show the anatomical planes as defined in the ACPC step.Target points are edited similarly to how the ACPC points are edited.For the bilateral case, once the target has been defined for one side,then when the user selects the target for the other side, the crosshairswill automatically jump to the mirror-image position. If the patient hassymmetric anatomy, this will save time in finding the equivalentposition. When using the brain atlas, the user may opt to show eitherjust the target structure (STN or GPi) or all structures. In eithercase, a tooltip (e.g., pop-up) can help the user to identify unfamiliarstructures. The user may also opt to scale and/or shift the brain atlasrelative to the patient image to make a better match. To do this, theuser may drag the white outline surrounding the brain atlas template.Fiber track structures and/or functional information of a patient'sbrain can be provided in a visually prominent manner (e.g., color codedor other visual presentation) for a surgeon's ease of reference. Thisinformation can also be selected or suppressed from views via a UIselection 32F (e.g., toolbar option) as shown in FIG. 4.

FIG. 20 is a screen shot of an exemplary screen display for a Trajectorystep in the Plan Entry workflow group. This step is used to find aclinically viable trajectory that determines the entry point on theskull typically via a grid such as that provided by the grid patch 50 g(FIG. 11). A visual warning can be displayed, e.g., a red warningmessage 30W on the top of the two top views and a red trajectory line30R) can be used to indicate that the selected trajectory does notintersect the grid. In operation, upon entering this step, theworkstation 30 can automatically search through the image volume for themarking grid(s) 50 g. It can be configured to position the initialtrajectory such that it runs through the middle of the grid 50 g. If theuser moves the trajectory such that the entry point is not on the grid,a warning 30W is displayed.

The top two views of FIG. 20 show the coronal and sagittal views alignedalong the current trajectory line. The user drags the trajectory lineand it rotates freely about the target point. The bottom-left view showsthe plane perpendicular to the trajectory at the level of the green linein the coronal and sagittal views. This is the “probe's eye” view. Toadvance the probe's eye view along the trajectory, in addition todragging the green line along the trajectory line or using themousewheel, onscreen VCR-style controls can provide an animatedfly-through.

FIG. 21 illustrates a (pop-up) warning 30W′ that is automaticallygenerated when a user selects a trajectory that may be blocked by thescanner bore wall. That is, if the user sets a trajectory such that thescanner bore will interfere with the insertion of the probe, a warningis displayed. This calculation is based on the bore size, currenttrajectory angles, and pre-configured values for the size of the probe50 a/50 s/52, canula 60, and frame/trajectory guide 50 t (FIG. 5).Similar to the target step, in the bilateral case once the trajectoryhas been set on one side, the initial default for the other side can bea mirror-image trajectory to start the user closer to a more a likelytrajectory. On saving the trajectory, the step automatically finds thesurface of the skull along the planned/selected trajectory, identifiesthe coordinates on the grid and stores that location as the entry point.

FIG. 22 illustrates an exemplary grid 50 g shown overlying a patient'sskull on a display 32 (without annotation lines), illustratingcoordinates for selecting an entry location (shown as columns 1-6 androws A-F) with a left STN entry location. FIG. 23 shows the same screenview as FIG. 22 but with optional annotation grid lines. Typically, auser can see the grid coordinates clearly enough that the optionaloverlay grid lines are not required in order to identify the gridelements. However, in some embodiments, as shown a UI will allow a userto display the lines.

FIG. 24 is an exemplary screen shot of a Plan Target Group workflow withthe ACPC step selected. This workflow group is used to preciselydetermine target points after one burr hole has been formed for aunilateral procedure or both burr-holes have been formed for bilateralprocedures (the surgical entries have been burred and the framesattached). Previous planning is typically invalidated by brain shiftthat occurs with the loss of cerebral spinal fluid pressure. This stepis substantially similar to the Plan Entry ACPC step discussed above.The difference is that in addition to the whole-head volume, the usermay optionally also send one or more high-resolution slabs containingthe ACPC points. The user can use a thumbnail bar to select which datato use to display and edit the ACPC landmarks. FIG. 25 illustrates ascreen shot with a Plan Target/ACPC step showing slab data.

FIG. 26 is an exemplary screen shot of a Plan Target Group workflow withthe Define Target step selected. The brain images can be shown withblended volume and slab image data. This step is similar to the DefineTarget step in the Plan Entry group, but like the preceding step it alsosupports high-resolution slabs to increase the precision with which thetarget can be defined. Thus, this step has the ability to show a blendedimage using data from both the volume and a high-resolution slab. Aslider 30S (shown to right under the word “blend”) in the UI allows theuser to control the ratio of how much of the image comes from eithersource.

FIG. 27 is a screen shot of a Trajectory step in the Plan Targetworkflow group. This step is similar to the Plan Entry/Trajectory step,but in this case this step is typically only used to review thetrajectory. The entry point cannot be changed since the hole has beenburred and the frame attached. Also, like the preceding step, this cansupport the use of high-resolution slabs and can blend between thevolume and the slab. On entering this step, the software canautomatically search through the whole-head volume and find the framemarker fiducials. From these, the system 10 and/or circuit 30 c candetermine the frame locations and orientation and uses this to calculatethe actual entry point on the head. This is used along with the targetfrom the previous step to determine the trajectory. Otherwise, thetrajectory may be reviewed as described above in the PlanEntry/Trajectory step.

FIG. 28 is a screen shot of a Navigate workflow group with the InitiateNavigation step selected. This visualization shows the proximal canulaslab. On entering this group, the user has already burred the entryhole, attached the frame, and finalized their planned targets. Thisgroup will guide the user through aligning the canula 60 (FIG. 8) tomatch the planned trajectory and inserting the probe through the canulato the correct depth. This step is used to determine the initialphysical location of the canula. The user acquires a scan through thetop of the canula and another through the bottom. The circuit 30 c(e.g., software) automatically finds the canula in each slab anddetermines its position and orientation in space. FIG. 29 illustratesthe distal canula slab in the Navigate/Initiate Navigation step.

FIG. 30 is a screen shot of a Navigate workflow group with the AlignCanula step selected. This step is used to physically align the canula60 (FIG. 8) to the planned trajectory. The user iteratively adjusts thecanula angulation via the pitch and roll control knobs as they rapidlyre-acquire an image through the top of the canula 60 p. With eachupdate, the circuit 30 c (e.g., software) calculates the position of thecanula 60 and displays an annotation showing where it's currentlypointing on the target plane. FIG. 30 illustrates that user feedbacksuch as a prompt over overlay or a tooltip-style pop-up can tell theuser which control to turn and which direction. In some embodiments, asshown, annotations can be drawn as circles corresponding to the probediameter. The circle with the crosshair is the planned target, the othercircle is the current projected point based on the trajectory of thecanula. The lines in between show the relative amount of pitch and rollto apply and the text can specify which known to turn and in whichdirection (shown as “turn pitch wheel to the left”).

FIG. 31 illustrates a screen shot from an exemplary Navigate/InsertProbe step. This screen shot illustrates coronal and sagittal views tothe target (e.g., STN) and can provide a set depth stop dimension (shownon the upper right hand side of the UI). This step allows the user tosee how well the probe is following the trajectory as it is inserted.The user may opt to scan Coronal and Sagittal slabs along the probe tovisually determine the probe alignment in those planes. The user canalso scan perpendicular to the probe. In that case, the circuit 30 c(e.g., software) can automatically identify where the probe is in theslab and it then shows a projection of the current path onto the targetplane to indicate the degree and direction of error if the current pathis continued. FIG. 32 illustrates an axial slab and projected point witha projected error if the current trajectory continues (the probe isshown in the right image offset by 4.6 mm and the offset is also notedon the UI as “Projected Error”. The user can perform these scansmultiple times during the insertion. The automatic segmentation of theprobe and the display of the projected target on the target planeprovide fully-automatic support for verifying the current path. TheCoronal/Sagittal views can provide the physician with a visualconfirmation of the probe path that doesn't depend on softwaresegmentation.

FIG. 33 illustrates an exemplary screen shot of a Refine Placementworkflow group with the Target Revision step selected. This step canillustrate the target slab. After completing the initial insertion, theuser (e.g., physician) may find that either the placement doesn'tcorrespond sufficiently close or perfectly to the plan, or the plan wasnot correct. This may be particularly likely if an imaging probe (50 a)is used, since a user will be able to more clearly visualize structureslike the STN that are usually indistinct with external coils. Thisworkflow group can support functionality whereby the physician canwithdraw the probe and use the X and Y offset adjustments to obtain aparallel trajectory to a revised target. This step can prompt the useror otherwise acquire an image slab through the distal tip of the probe.(Optionally, this step may use the imaging probe). The step displays theslab and on it the user may opt to modify the target point to a newlocation or accept the current position as final.

FIG. 34 illustrates an exemplary screen shot of the Refine Placementworkflow group with the Adjust X-Y Offset step selected. This step isvery similar to the Navigate/Align Canula step described above. Theprimary difference is that instead of adjusting the angulation of thecanula 60, the user is adjusting a small X-Y offset to set the canula 60to a trajectory parallel to the original one. FIG. 34 shows the displaywith an visualization f the position of the probe tip relative to thetarget and with instructions on what physical adjustments to make toobtain the desired parallel trajectory (shown as “turn Y wheel to theright”) and the projected error (shown a 2.7 mm). FIG. 35 illustrates adetail of the adjust annotations and pop-up (shown as “turn X wheel tothe left”).

After the X-Y adjustments are made, the Insert Probe of the RefinePlacement workflow group is selected and carried out in the same manneras the Navigate/Insert Probe step described above.

FIG. 36 illustrates the Refine Placement workflow group with the“conclude procedure” step selected. This step occurs after all probeshave been inserted and have had their positions verified by thephysician. At this point, the UI can prompt them to insert both leadswhere implantable stimulation leads are to be placed (using the definedtrajectory) and can warn them not to perform any additional scans ifMRI-incompatible or potentially incompatible leads are used. As shown,the system 10 can be configured to define (and output to a user) ordepth stops to set the lead or other therapy or diagnostic device foreach STN or target site. The depth stops can be different for eachimplant location on the left and right targets (for bilateralprocedures) so that the electrodes of the leads or other components forother devices are positioned in the desired location.

FIG. 37 illustrates an example of a display that may be used for theADMIN workflow group. This group has one step that provides reportingand archive functionality. The report automatically documents the entireprocedure including annotations, measurements, and screen captures. Thecircuit 30 c can generate a full version and an anonymous version of thereport and may include a date as to when everything is archived to CD.

The circuit 30 c may also be configured to determine where individualelectrodes on the DBS leads are situated in ACPC coordinates. Given thetip position in MR coordinates (the circuit 30 c can ill in the plannedposition, but the user may change it) the user will provide a set ofoffset values that represent the distance of each electrode from thelead tip. In other embodiments, a lead type can be selected such as froma pull-down list and those values can automatically be input based onthe manufacturer and lead type (e.g., design thereof). The circuit 30 ccan be configured so that the UI displays the corresponding electrodepositions in ACPC coordinates.

FIG. 38 illustrates an example of a display with a UI that may be usedfor the ADMIN workflow group shown as—Admin Page/Electrode Offset dialogstep selected. This step may also be included in the ConcludeProcedure/step or provided as a separate workflow group. The electrodeoffset values may significantly speed up the process by which the pulsegenerator is programmed since the physician will know where theelectrodes are anatomically.

The system 10 may also include a decoupling/tuning circuit that allowsthe system to cooperate with an MRI scanner 20 and filters and the like.See, e.g., U.S. Pat. Nos. 6,701,176; 6,904,307 and U.S. PatentApplication Publication No. 2003/0050557, the contents of which arehereby incorporated by reference as if recited in full herein. As notedabove, one or more of the tools can include an intrabody MRI antenna 50a (FIG. 5) that is configured to pick-up MRI signals in local tissueduring an MRI procedure. The MRI antenna can be configured to reside onthe distal portion of the probe. In some embodiments, the antenna has afocal length or signal-receiving length of between about 1-5 cm, andtypically is configured to have a viewing length to receive MRI signalsfrom local tissue of between about 1-2.5 cm. The MRI antenna can beformed as comprising a coaxial and/or triaxial antenna. However, otherantenna configurations can be used, such as, for example, a whipantenna, a coil antenna, a loopless antenna, and/or a looped antenna.See, e.g., U.S. Pat. Nos. 5,699,801; 5,928,145; 6,263,229; 6,606,513;6,628,980; 6,284,971; 6,675,033; and 6,701,176, the contents of whichare hereby incorporated by reference as if recited in full herein. Seealso U.S. Patent Application Publication Nos. 2003/0050557;2004/0046557; and 2003/0028095, the contents of which are also herebyincorporated by reference as if recited in full herein.

In some embodiments, the implanted leads and/or intrabody tools can beconfigured to allow for safe MRI operation so as to reduce thelikelihood of undesired deposition of current or voltage in tissue. Theleads or tools can include RF chokes such as a series of axially spacedapart Balun circuits or other suitable circuit configurations. See,e.g., U.S. Pat. No. 6,284,971, the contents of which are herebyincorporated by reference as if recited in full herein, for additionaldescription of RF inhibiting coaxial cable that can inhibit RF inducedcurrent. The conductors connecting electrodes or other components on orin the tools can also include a series of back and forth segments (e.g.,the lead can turn on itself in a lengthwise direction a number of timesalong its length) and/or include high impedance circuits. See, e.g.,U.S. patent application Ser. Nos. 11/417,594; 12/047,602; and Ser. No.12/090,583, the contents of which are hereby incorporated by referenceas if recited in full herein.

Although not shown, in some embodiments, one or more of the surgicaltools can be configured with one or more lumens and exit ports thatdeliver desired cellular, biological, and/or drug therapeutics to thetarget area, such as the brain. The tools may also incorporatetransseptal needles, biopsy and/or injection needles as well as ablationmeans. The lumens, where used, may receive extendable needles that mayexit the probe from the distal end or from the sides, proximal, distal,or even, through the electrodes to precisely deliver cellular/biologicaltherapeutics to the desired anatomy target. This delivery configurationmay be a potential way to treat patients, where the cellular/biologicaltherapeutics can be delivered into the desired anatomy to modify theircellular function. The cells (e.g., stem cells) may improve function.MRI can typically be effectively used to monitor the efficacy and/ordelivery of the therapy.

The system 10 can include circuits and/modules that can comprisecomputer program code used to automatically or semi-automatically carryout operations to generate visualizations and provide output to a userto facilitate MRI-guided diagnostic and therapy procedures. FIG. 39 is aschematic illustration of a circuit or data processing system that canbe used with the system 10. The circuits and/or data processing systemsmay be incorporated in one or more digital signal processors in anysuitable device or devices. As shown in FIG. 39, the processor 410communicates with an MRI scanner 20 and with memory 414 via anaddress/data bus 448. The processor 410 can be any commerciallyavailable or custom microprocessor. The memory 414 is representative ofthe overall hierarchy of memory devices containing the software and dataused to implement the functionality of the data processing system. Thememory 414 can include, but is not limited to, the following types ofdevices: cache, ROM, PROM, EPROM, EEPROM, flash memory, SRAM, and DRAM.

As shown in FIG. 39 illustrates that the memory 414 may include severalcategories of software and data used in the data processing system: theoperating system 452; the application programs 454; the input/output(I/O) device drivers 458; and data 456. The data 456 can also includepredefined characteristics of different surgical tools and patient imagedata 455. FIG. 39 also illustrates the application programs 454 caninclude a Visualization Module 450, Interventional Tool Data Module 451,a Tool Segmentation Module 452 (such as segmentation modules for a gridpatch, a targeting canula, and a trajectory guide frame and/or base),and a workflow group User Interface Module 453 (that facilitates useractions and provides guidance to obtain a desired trajectory such asphysical adjustments to achieve same).

As will be appreciated by those of skill in the art, the operatingsystems 452 may be any operating system suitable for use with a dataprocessing system, such as OS/2, AIX, DOS, OS/390 or System390 fromInternational Business Machines Corporation, Armonk, N.Y., Windows CE,Windows NT, Windows95, Windows98, Windows2000 or other Windows versionsfrom Microsoft Corporation, Redmond, Wash., Unix or Linux or FreeBSD,Palm OS from Palm, Inc., Mac OS from Apple Computer, LabView, orproprietary operating systems. The I/O device drivers 458 typicallyinclude software routines accessed through the operating system 452 bythe application programs 454 to communicate with devices such as I/Odata port(s), data storage 456 and certain memory 414 components. Theapplication programs 454 are illustrative of the programs that implementthe various features of the data processing system and can include atleast one application, which supports operations according toembodiments of the present invention. Finally, the data 456 representsthe static and dynamic data used by the application programs 454, theoperating system 452, the I/O device drivers 458, and other softwareprograms that may reside in the memory 414.

While the present invention is illustrated, for example, with referenceto the Modules 450-453 being application programs in FIG. 39, as will beappreciated by those of skill in the art, other configurations may alsobe utilized while still benefiting from the teachings of the presentinvention. For example, the Modules 450-453 and/or may also beincorporated into the operating system 452, the I/O device drivers 458or other such logical division of the data processing system. Thus, thepresent invention should not be construed as limited to theconfiguration of FIG. 39 which is intended to encompass anyconfiguration capable of carrying out the operations described herein.Further, one or more of modules, i.e., Modules 450-453 can communicatewith or be incorporated totally or partially in other components, suchas a workstation, an MRI scanner, an interface device. Typically, theworkstation 30 will include the modules 450-453 and the MR scanner withinclude a module that communicates with the workstation 30 and can pushimage data thereto.

The I/O data port can be used to transfer information between the dataprocessing system, the circuit 30 c or workstation 30, the MRI scanner20, and another computer system or a network (e.g., the Internet) or toother devices controlled by or in communication with the processor.These components may be conventional components such as those used inmany conventional data processing systems, which may be configured inaccordance with the present invention to operate as described herein.

In the drawings and specification, there have been disclosed embodimentsof the invention and, although specific terms are employed, they areused in a generic and descriptive sense only and not for purposes oflimitation, the scope of the invention being set forth in the followingclaims. Thus, the foregoing is illustrative of the present invention andis not to be construed as limiting thereof. More particularly, theworkflow steps may be carried out in a different manner, in a differentorder and/or with other workflow steps or may omit some or replace someworkflow steps with other steps. Although a few exemplary embodiments ofthis invention have been described, those skilled in the art willreadily appreciate that many modifications are possible in the exemplaryembodiments without materially departing from the novel teachings andadvantages of this invention. Accordingly, all such modifications areintended to be included within the scope of this invention as defined inthe claims. In the claims, means-plus-function clauses, where used, areintended to cover the structures described herein as performing therecited function and not only structural equivalents but also equivalentstructures. Therefore, it is to be understood that the foregoing isillustrative of the present invention and is not to be construed aslimited to the specific embodiments disclosed, and that modifications tothe disclosed embodiments, as well as other embodiments, are intended tobe included within the scope of the appended claims. The invention isdefined by the following claims, with equivalents of the claims to beincluded therein.

That which is claimed is:
 1. A computer program product for facilitatingan MRI-guided surgical procedure, the computer program productcomprising: a non-transitory computer readable storage medium havingcomputer readable program code embodied in the medium, thecomputer-readable program code comprising: computer readable programcode that comprises predefined physical data of a plurality of differentsurgical tools; computer readable program code that obtains MR imagedata of a patient; computer readable program code that generatesmulti-dimensional visualizations using the predefined physical data ofthe different surgical tools and data from the obtained MR images of thepatient in substantially real time during the MRI-guided surgicalprocedure; and computer readable program code that provides a UserInterface to a display that defines workflow progression for theMRI-guided surgical procedure and allows a user to select steps in theworkflow, wherein the computer readable program code that comprisespredefined physical data of a plurality of different surgical toolsincludes computer readable program code associated with a trajectoryguide as one of the surgical tools, the trajectory guide comprisingfiducial markers in a fixed geometric relationship, the trajectory guideconfigured to define a trajectory path for a subsurface brain target inthe patient, the trajectory guide having a base that affixes to apatient's skull, wherein the computer program product further comprisescomputer readable program code that segments the obtained MR image dataincluding computer readable program code that segments the obtained MRimage data to locate the fiducial markers of the trajectory guide andidentify an orientation of the trajectory guide.
 2. The computer programproduct of claim 1, wherein the computer readable program code thatobtains MR image data of the patient is configured to obtain MR imagedata of patient function, and wherein the computer readable program codethat generates the visualizations also shows patient function includingactive regions in a brain of the patient based on fMRI and/or patientstimulation.
 3. The computer program product of claim 1, furthercomprising computer readable program code that selectively displaysbrain fiber tracks of the patient in at least some of the visualizationson at least one display.
 4. The computer program product of claim 1,wherein the computer readable program code that segments the image datais configured to segment the image data while the patient is in ahigh-magnetic field of an MRI scanner using the predefined physicaldata, wherein the predefined physical data comprises predefined physicalcharacteristics of a flexible grid attached to a skull of the patient;and computer readable program code that deforms an electronic model ofthe grid to fit a head surface of the patient and identify associatedvertices.
 5. The computer program product of claim 1, wherein thecomputer readable program code that provides the User Interface thatdefines workflow progression for the MRI-guided surgical procedurecomprises a series of selectable workflow groups including “start”,“plan entry”, “plan target”, “navigate”, and “refine” that is used toguide the MRI-guided surgical procedure resulting in delivering atherapy after the “refine” workflow group.
 6. The computer programproduct of claim 5, wherein the computer readable program code thatprovides the User Interface also provides a “bilateral” selectionoption.
 7. The computer program product of claim 5, wherein the computerreadable program code that provides the User Interface also includes an“Administrative” workflow group that electronically generates a medicalreport automatically summarizing clinical information regarding thepatient and certain surgical information including at least a pluralityof the following: (a) AC, PC, and MSP points in MR space (both detectedand user-specified, if user modified); (b) planned and corrected targetsin both MR and ACPC space; (c) elapsed time for the procedure; and (d)screenshots taken during the procedure.
 8. The computer program productof claim 1, wherein the computer readable program code that provides theUser Interface further comprises computer readable program code thatallows a user to select different intrabody procedures including aunilateral or bilateral procedure and a desired intrabody target, then,if a bilateral procedure is selected, the computer readable program codeprovides a toolbar with left and right workflow steps.
 9. The computerprogram product of claim 1, further comprising computer readable programcode that generates a different workflow group when a bilateral optionis selected so as to display workflow steps that guides a user tocomplete grid entry locations for both bilateral sides, hole formationfor both sides and trajectory frame attachment to both sides beforeproceeding to a “plan target” step due to brain shift and beforedirecting a patient to be returned to an imaging location.
 10. Thecomputer program product of claim 1, further comprising: computerreadable program code that presents on a display, a user-selectabletrajectory line to a deep brain location that intersects a flexible gridon a patient's skull and defines a location on the grid for marking aburr entry hole based on the desired trajectory line; and computerreadable program code that generates an audible and/or visual warningwhen a user selects a trajectory line that does not intersect the grid.11. The computer program product of claim 1, further comprising computerreadable program code that accepts input of an identifier associatedwith the tools and blocks use of a surgical system if the identifierindicates that it is not an authorized tool or that the at least onetool has a version that is not compatible with the surgical system. 12.The computer program product of claim 1, further comprising: computerreadable program code configured to analyze data regarding a bore sizeof a scanner being used for the MRI-guided surgical procedure of thepatient; computer readable program code configured to monitor for aphysical limitation or interference of a surgical tool based on: (a)pre-defined physical characteristics of the surgical tool; (b) scannerbore size; and (c) patient size; and computer readable program codeconfigured to generate an audible or visual warning or an audible andvisual warning when one or more of the surgical tools will be blocked byphysical interference with a wall defining at least a portion of thebore size of the scanner.
 13. The computer program product of claim 1,further comprising: computer readable program code that identifies aposition and orientation of a flexible patch as one of the surgicaltools based on predefined physical characteristics of the patch, thepatch comprising a grid and is adapted to reside on the patient;computer readable program code that deforms an electronic model of thepatch to fit curvature of a skull of the patient; and computer readableprogram code that displays a visual overlay of the deformed electronicmodel of the patch on the skull of the patient on at least one display.14. The computer program product of claim 1, further comprising computerreadable program code that: segments the image data while the patient isin a high-magnetic field of an MRI scanner using predefined physicalcharacteristics of a flexible patch with a grid attached to a skull ofthe patient and of a trajectory guide as two of the surgical tools withthe predefined physical data; deforms an electronic model of theflexible patch with the grid to fit a head surface of the patient andidentify associated vertices; calculates user adjustments to move atleast one of a pitch, roll, X or Y actuator to adjust a trajectory of atrajectory guide to provide a desired intrabody trajectory to a targetsite; and displays the calculated user adjustments to at least onedisplay associated with an MRI suite to thereby provide a user withadjustment data regarding actuator adjustment for at least one of apitch, roll, X or Y actuator of the trajectory guide to achieve thedesired intrabody trajectory thereby facilitating an MRI-guided surgicalprocedure.
 15. The computer program product of claim 1, wherein thepredefined physical data comprises predefined characteristics of aflexible patch as one of the surgical tools, wherein the generatedvisualizations include a visualization presented on a display whichshows the flexible patch as an overlay on the patient with defined gridcoordinates for a surgical entry site.
 16. The computer program productof claim 1, wherein the computer readable program code that provides theUser Interface on a display is configured to allow a user to select abilateral procedure, and in response thereto, the User Interfacedisplays workflow steps that guides a user to complete grid entrylocations for two sides of a brain, hole formation for both sides andtrajectory frame attachment to both sides before proceeding to a “plantarget” step due to brain shift and before directing a patient to bereturned to an imaging location in a bore of a magnet of an MRI scanner.17. The computer program product of claim 1, wherein the computerreadable program code that comprises predefined physical data of aplurality of different surgical tools includes an imaging probe with anintrabody antenna as one of the different surgical tools, the imagingprobe configured to collect small field, high-resolution image data, andwherein the computer program product further comprises computer readableprogram code that is configured to electronically apply a correction toreduce intensity distortion associated with image data collected fromthe imaging probe.
 18. The computer program product of claim 1, whereinthe trajectory guide fiducial markers are circumferentially spaced apartand positioned relative to each other such that at least two are closertogether than another to define an affirmative orientation of thetrajectory guide.
 19. The computer program product of claim 18, whereinthe fiducial markers comprise three fluid-filled annular fiducialmarkers.
 20. The computer program product of claim 1, further comprisingcomputer readable program code that generates color codedelectroanatomical visualizations of target anatomy in substantiallyreal-time as at least some of the generated visualizations, using atleast one of: (a) electrical signals obtained from electrodes associatedwith one or more of the surgical tools, correlated to time and positionof the electrodes to render visualizations to illustrate neuralelectrical potentials and locations; or (b) patient functional dataincluding fMRI data or MRI image data or fMRI and MRI image data showingelectrical activity in response to a stimulation.
 21. The computerprogram product of claim 1, wherein the generated visualizationscomprise a spatially encoded position and orientation of a tool of theplurality of different surgical tools.